which sample types normal tissue or which are cancer tissue?

[Bishal Imtiaz]

I have downloaded "TcgaTargetGTEX_phenotype.txt"  from https://toil.xenahubs.net/download/TcgaTargetGTEX_phenotype.txt.gz; Full metadata. Here i found 17 unique sample types 

Primary Tumor

Solid Tissue Normal

Recurrent Tumor

Metastatic

Additional - New Primary

Additional Metastatic

Primary Blood Derived Cancer - Peripheral Blood

Control Analyte

Cell Line

Normal Tissue

Recurrent Solid Tumor

Primary Solid Tumor

Recurrent Blood Derived Cancer - Bone Marrow

Primary Blood Derived Cancer - Bone Marrow

Post treatment Blood Cancer - Bone Marrow

Post treatment Blood Cancer - Blood

Recurrent Blood Derived Cancer - Peripheral Blood

I only need to classify either tumor/cancer tissue or normal tissue. From these 17 sample types i can say primary tumor recurrent.tumor etc,these are not normal tissue. But in case of Solid Tissue normal or Cell Line i can't understand if these are normal tissue or not?

The question is from those 17 sample types which ones are normal tissue i,e which ones are not tumor/cancer tissue? what does these sample types mean?

Thank you

[Bishal Imtiaz]

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[Mary Goldman]

Hi Bishal,

The normal tissue types come from different projects. Some come from matched normal in TCGA and some are not matched normal from GTEx.  You will need to combine the field below with the project (i.e. TCGA, TARGET or GTEx) to see which is which. If you have further questions about what a sample type means for a particular project, I would recommend going to the project sources for more information.

Best,
Mary
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Mary Goldman
UCSC Xena

UC Santa Cruz Genomics Institute

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